Theoretical study of sequence-dependent nanopore unzipping of DNA

Biophysical Journal

Volumn 94, Issue 7, 2008, Pages 2716-2724

  Bockelmann, Ulrich ^a   Viasnoff, V ^a  

^a CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NANOMATERIAL;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; ELECTROPORATION; LIPID BILAYER; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; POROSITY; RADIATION EXPOSURE; ULTRASTRUCTURE;

BASE SEQUENCE; COMPUTER SIMULATION; DNA; ELECTROPORATION; LIPID BILAYERS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NANOSTRUCTURES; NUCLEIC ACID CONFORMATION; POROSITY;

EID: 41649106512     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.111732     Document Type: Article

References (37)

1. Kasianowicz, J., E. Brandin, D. Branton, and D. Deamer. 1996. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA. 98:13770-13773.
2. Meller, A., L. Nivon, E. Brandin, J. Golovchenko, and D. Branton. 2000. Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. USA. 97:1079-1084.
3. Akeson, M., D. Branton, J. J. Kasianowicz, E. Brandin, and D. Deamer. 1999. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77: 3227-3233.
4. Ashkenasy, N., J. Sánchez-Quesada, H. Bayley, and M. R. Ghadiri. 2005. Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores. Angew. Chem. Int. Ed. 44: 1401-1404.
5. Sauer-Budge, A. F., J. A. Nyamwanda, D. K. Lubensky, and D. Branton. 2003. Unzipping kinetics of double-stranded DNA in a nanopore. Phys. Rev. Lett. 90:238101.
6. Mathé, J., H. Visram, V. Viasnoff, Y. Rabin, and A. Meller. 2004. Nanopore unzipping of individual DNA hairpin molecules. Biophys. J. 87:3205-3212.
7. Mathé, J., A. Arinstein, Y. Rabin, and A. Meller. 2006. Equilibrium and irreversible unzipping of DNA in a nanopore. Europhys. Lett. 73: 128-134.
8. Vercoutere, W., S. Winter-Hilt, H. Olsen, D. Deamer, D. Haussler, and M. Akeson. 2001. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat. Biotechnol. 19:248-252.
9. Aksimentiev, A., and K. Schulten. 2005. Imaging α-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map. Biophys. J. 88:3745-3761.
10. Matysiak, S., A. Montensi, M. Pasquali, A. B. Kolomeisky, and C. Clementi. 2006. Dynamics of Polymer Translocation through nanopores: theory meets experiment. Phys. Rev. Lett. 96:118103.
11. Muthukumar, M. 2007. Mechanism of DNA transport through pores. Annu. Rev. Biophys. Biomol. Struct. 36:435-450.
12. Kafri, Y., D. K. Lubensky, and D. R. Nelson. 2004. Dynamics of Molecular Motors and Polymer Translocation with Sequence Heterogeneity. Biophys. J. 86:3373-3391.
13. Gerland, U., R. Bundschuh, and T. Hwa. 2004. Translocation of structured polynucleotides through nanopores. Phys. Biol. 1:19-26.
14. Lakatos, G., T. Chou, B. Bergersen, and G. N. Patey. 2005. First passage times of driven DNA hairpin unzipping. Phys. Biol. 2:166-174.
15. Dudko, O. K., J. Mathé, A. Szabo, A. Meller, and G. Hummer. 2007. Extracting kinetics from single-molecule force spectroscopy: nanopore unzipping of DNA hairpins. Biophys. J. 92:4188-4195.
16. Bundschuh, R., and U. Gerland. 2005. Coupled dynamics of RNA folding and nanopore translocation. Phys. Rev. Lett. 95:208104.
17. Zhang, J., and B. I. Shklovskii. 2007. Effective charge and free energy of DNA inside on ion channel. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 75:021906.
18. Kotsev, S., and A. B. Kolomeisky. 2006. Effect of orientation in translocation of polymers through nanopores. J. Chem. Phys. 125:084906.
19. SantaLucia, J. 1998. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA. 95:1460-1465.
20. SantaLucia, J., and D. Hicks. 2004. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33:415-440.
21. Manning, J. S. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11:179-246.
22. Reference deleted in proof.
23. Cocco, S., J. F. Marko, and R. Monasson. 2003. Slow nucleic acid unzipping kinetics from sequence-defined barriers. Eur. Phys. J. E. 10:153-161.
24. Goddard, N. L., G. Bonnet, O. Krichevsky, and A. Libchaber. 2000. Sequence-dependent rigidity of single-stranded DNA. Phys. Rev. Lett. 85:2400-2403.
25. Meller, A., L. Nivon, and D. Branton. 2001. Voltage-driven DNA translocation through a nanopore. Phys. Rev. Lett. 86:3435-3438.
26. Viovy, J.-L., Ch. Heller, F. Caron, Ph. Cluzel, and D. Chatenay. 1994. Sequencing of DNA by mechanical opening of the double helix: a theoretical evaluation. C. R. Acad. Sci. Paris. 317:795-800.
27. Thompson, R. E., and E. D. Siggia. 1995. Physical limits on the mechanical measurement of the secondary structure of biomolecules. Europhys. Lett. 31:335-340.
28. Lubensky, D. K., and D. R. Nelson. 2000. Pulling pinned polymers and unzipping DNA. Phys. Rev. Lett. 85:1572-1575.
29. Essevaz-Roulet, B., U. Bockelmann, and F. Heslot. 1997. Mechanical separation of the complementary strands of DNA. Proc. Natl. Acad. Sci. USA. 94:11935-11940.
30. Bockelmann, U., Ph. Thomen, B. Essevaz-Roulet, and F. Heslot. 2002. Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. Biophys. J. 82:1537-1553.
31. Bockelmann, U., Ph. Thomen, and F. Heslot. 2004. Dynamics of the DNA duplex formation studied by single molecule force measurements. Biophys. J. 87:3388-3396.
32. Danilowicz C., V. W. Coljee, C. Bouzigues, D. K. Lubensky, D. R. Nelson, and M. Prentiss. 2003. DNA unzipped under a constant force exhibits multiple metastable intermediates. Proc. Natl. Acad. Sci. USA. 100:1694-1699.
33. Bockelmann, U., B. Essevaz-Roulet, and F. Heslot. 1997. Molecular stick-slip motion revealed by opening DNA with picoNewton forces. Phys. Rev. Lett. 79:4489-4492.
34. Bouchaud, J. P., and A. Georges. 1990. Anomalous diffusion in disordered media: statistical mechanisms, models and physical applications. Phys. Rep. 4:127.
35. Mathé, J., A. Aksimentiev, D. R. Nelson, K. Schulten, and A. Meller. 2005. Orientation discrimination of single-stranded DNA inside the a-hemolysin membrane channel. Proc. Natl. Acad. Sci. USA. 102: 12377-12382.
36. Tinland, B., A. Pluen, J. Sturm, and G. Weill. 1997. Persistence length of single-stranded DNA. Macromolecules. 30:5763-5765.
37. Record, M. T., Jr., C. F. Anderson, and T. M. Lohmann. 1978. Thermodynamics analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the role of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11:103-178.